Ah, okay thanks very much! I thought-sure I had the most recent version, but apparently not. Still there's one quirk...
x2top -f HexA.gro -o HexA.top -r HexA.rtp -alldih ...This works to generate a topology file, but still, the program is seg-faulting before writing out the residue type file (*.rtp). I'm not yet sure if I can get by without the .rtp since hexadecane (C16) won't likely be a recognized residue type. Any ideas why this is seg-faulting or how I can get around the fact that restype (C16) won't be recognized? Thanks so much, -Adam On 10/10/07, David van der Spoel <[EMAIL PROTECTED]> wrote: > > Adam Fraser wrote: > > Yes I tried this and it doesn't work for me. I get: > > > > Fatal error: > > Library file ffG53a6.n2t not found in current dir nor in default > > directories. > > (You can set the directories to search with the GMXLIB path variable) > > > > did you use 3.3.2 ? The default and only supported FF there is OPLS. For > GROMOS variants you can try the prodrg webserver. > > > Also, doesn't x2top take in a gro file? (not a pdb) I wrote a script > > that converts pdb to gro, and I still get the above error. > > > > -Adam > > > > On 10/10/07, * David van der Spoel* <[EMAIL PROTECTED] > > <mailto:[EMAIL PROTECTED]>> wrote: > > > > Adam Fraser wrote: > > > Hello, > > > > > > I'm very new to Gromacs, and I am interested in simulating the > > > interactions of 2 hexadecane (C16H34) molecules in water (SPC/E > > > specificall). I've spent some time experimenting with tutorials > in > > > Gromacs, but I've found little help in non-protein simulations > > like this > > > one. > > > > > > I've built topologies for hexadecane compatible with NAMD, so I > > figure I > > > should be able to do the same in Gromacs but I'm fuzzy on how to > go > > > about doing so (what files to edit). I was also hoping to get > some > > > input on which forcefield would be best for this sort of system. > > > > > > I'd greatly appreciate it if someone could give me some pointers > > on how > > > to get started here. > > > > > > Thanks very much, > > > Adam > > > > > if you have a pdb file you can run x2top (3.3.2 only). > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > > > _______________________________________________ > > > gmx-users mailing list [email protected] > > <mailto:[email protected]> > > > http://www.gromacs.org/mailman/listinfo/gmx-users > > > Please search the archive at http://www.gromacs.org/search before > > posting! > > > Please don't post (un)subscribe requests to the list. Use the > > > www interface or send it to [EMAIL PROTECTED] > > <mailto:[EMAIL PROTECTED]>. > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > <http://www.gromacs.org/mailing_lists/users.php> > > > > > > -- > > David van der Spoel, Ph.D. > > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala > University. > > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: > +4618511755. > > [EMAIL PROTECTED] > > <mailto:[EMAIL PROTECTED]> [EMAIL PROTECTED] > > <mailto:[EMAIL PROTECTED]> http://folding.bmc.uu.se > > _______________________________________________ > > gmx-users mailing list [email protected] > > <mailto:[email protected]> > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > <mailto:[EMAIL PROTECTED]>. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > gmx-users mailing list [email protected] > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > David van der Spoel, Ph.D. > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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